User:Eric Martz/Sandbox 3

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(→Changing a Checkbox - ed)
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# All chains are colored and spacefilled, not just one chain. This includes both sequence-identical chains, and sequence different chains.
# All chains are colored and spacefilled, not just one chain. This includes both sequence-identical chains, and sequence different chains.
# The 10 color grade groups of residues are selected only once, for all chains, as shown in the example script below.
# The 10 color grade groups of residues are selected only once, for all chains, as shown in the example script below.
 +
 +
<b>MASTER SCRIPT</b>
 +
 +
<tt><pre>
 +
# insert allRenderingsOff script (already in use for NMR)
 +
 +
select hetero and not water
 +
spacefill 0.5
 +
wireframe 0.3
 +
color cpk
 +
dots
 +
 +
script 2hhd_consurf.spt # from pre-calculated ConSurf dataset, one per PDB code
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 +
select protein
 +
backbone 0.4
 +
color backbone [xc8c8c8]
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</pre></tt>

Revision as of 00:58, 29 June 2008

Contents

ConSurf Prototype

PDB ID 2hhd

Drag the structure with the mouse to rotate
2hhd, resolution 2.20Å ()
Ligands: ,
Resources: FirstGlance, OCA, RCSB, PDBsum
Coordinates: save as pdb, mmCIF, xml



Scenes

Opening the proposed Evolutionary Conservation section below the molecule would automatically color all chains by ConSurf, and spacefill them. Checkboxes in this section, one per chain, would be checked when the section is first opened. Unchecking a given chain would render it as a gray backbone (as in ConSurf). Ligands will be ball and stick, with dot surfaces, colored by element (as in ConSurf; oops, forgot to do the sulfates in some scenes).

  • (2 alphas, A and C, and 2 betas, B and D, in 2HHD).
  • (one alpha, one beta)
  • (both alphas)

User Interface & Color Key

Below are non-interactive mockups just to suggest the look for a user interface.

  • Links do not work.
  • The color key image should be centered (I could not get it centered in the mockup).
  • [✓] represents a checkbox. When checked, it will color the chain by conservation, and spacefill it. When unchecked, that chain will become a gray backbone trace.
  • The link to Explanation would go to a Proteopedia page of explanation. It might be a revised version of Conservation, Evolutionary.


Before expanding this section, it could look like this:

Evolutionary Conservation:                           [show]


After expanding, it could look like this:

Scripts

When the Evolutionary Conservation block is expanded, a master script is run that colors and spacefills all chains.

Changing a Checkbox

After a checkbox is changed, the currently checked chains are put into this script: 

select protein
spacefill off
select (:a,:c) # LIST OF CHECKED CHAINS
spacefill

Master ConSurf Script

The master script will need to be generated by ConSurf for each PDB code. It differs in a few minor ways from the per-chain scripts currently being generated.

  1. All chains are colored and spacefilled, not just one chain. This includes both sequence-identical chains, and sequence different chains.
  2. The 10 color grade groups of residues are selected only once, for all chains, as shown in the example script below.

MASTER SCRIPT 

# insert allRenderingsOff script (already in use for NMR)

select hetero and not water
spacefill 0.5
wireframe 0.3
color cpk
dots

script 2hhd_consurf.spt # from pre-calculated ConSurf dataset, one per PDB code

select protein
backbone 0.4
color backbone [xc8c8c8]

Proteopedia Page Contributors and Editors (what is this?)

Eric Martz, Jaime Prilusky

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